MisCoTo

How to compare the metabolic network of bacterial community with a host (here an alga)

# 1. Alignment of the metabolic networks

First, make sure that you installed **python 3.6**. Then you will be able to **install miscoto** :

    pip3 install pyasp (or pip3 install pyasp --no-cache-dir)
    pip3 install miscoto

After, the different miscoto command line can be run :

## 1.1 the command which allows you to extract new producible compounds 

    miscoto_scopes -m host.sbml -b output_folder/sbml/ -s seeds.xml -t targets.xml

Seeds = set of starting compounds

Targets = set of targeted compounds

## 1.2 the command which gives optimal solution

    miscoto_mincom -m host.sbml -b output_folder/sbml/ -s seeds.xml -t targets.xml -o soup

Here the tagets correspond to the compounds found with the miscoto_scopes command. 
you should see the selected bacteria in this step with their IDs/names

## 1.3 the command which Displays all the possible solution

    miscoto_mincom -m host.sbml -b output_folder/sbml/ -s seeds.xml -t targets.xml -o soup --enumeration

## 1.4 the command which indicates organisms shared by all the solutions

    miscoto_mincom -m host.sbml -b output_folder/sbml/ -s seeds.xml -t targets.xml -o soup --intersection

## 1.5 the command which points out a fusion of all the solutions (all the bacteria that participate to at least one solution)

    miscoto_mincom -m host.sbml -b output_folder/sbml/ -s seeds.xml -t targets.xml -o soup --union


For more details and information check out the link  https://github.com/cfrioux/miscoto